Wolbachia are maternally transmitted bacteria that alter their arthropod hosts’ reproduction in various ways, including parthenogenesis induction (PI). Wolbachia-induced parthenogenesis can have drastic effects on the genetic structure of its host because it potentially reduces populations to clones without genetic exchange. However, Wolbachia-induced parthenogenesis does not inevitably result in a reduction of genetic variation of infected populations vs. uninfected populations, because the parthenogenetic populations are initially derived from uninfected populations and can thus show similar genetic variation. Here we investigate these issues in infected and uninfected populations of the Drosophila parasitoid Leptopilina clavipes in western Europe. Wasps from 19 sites in the Netherlands, France and northern Spain were screened for Wolbachia and analysed using amplified fragment length polymorphism (AFLP) markers. All the populations from the Netherlands and mid-France were infected with the same two strains of Wolbachia, whereas populations from the Pyrenees were not infected. The infected and uninfected populations show identical levels of genetic variation, but have clearly diverged genetically, indicating the presence of a barrier that prevents gene flow. Within the infected wasps two distinct genotypes were found at multiple localities, indicating the coexistence of multiple clones. The conditions promoting clonal coexistence in L. clavipes are discussed.